Atlantis Reborn
by SassyJ
Summary: Almost four years after Sheppard and McKay were yanked off Atlantis, things have not gone so well for the city without them. The IOA and SGC want them back, and O'Neill is sent to offer them anything. But after the way they were treated will he succeed? (Shep Whump)
1. The Long and Winding Road

General Jack O'Neill ran a finger under his suddenly too tight collar and glanced in the rear view mirror for what had to be the nineteenth time in as many minutes. Caught Colonel Samantha Carter's clear blue-eyed gaze and almost blushed. "Are we really going to do this?"

"General, we have no other choice. No one else knows the city like them." Woolsey shifted uncomfortably in his seat. "It's been three years. Surely…" He trailed off.

O'Neill glanced across at Daniel Jackson, sitting so silently in the passenger seat. "What do you think?" he asked.

Daniel looked down at his hands. "I think that… on a personal level, this is a bad idea. McKay is going to eat us alive, that is of course if we can get in through the front gate. And Sheppard…" he closed his eyes for a second, remembering, "well no one here knows for certain what the Colonel's condition is." He stressed the title, and shot his friend a hard stare. "I know this is a military operation but frankly, you and Carter showing up here in full uniform is probably the wrong thing to do."

O'Neill swallowed. He knew that, but he also knew that if they could get McKay and Sheppard to even consider whether they were going with this, they needed to get them to make peace with the military again. Even though it was the military, at the IOA's urging that had tried to destroy Lt. Colonel John Sheppard before.

Three years. He doubted that was enough time for either man to forget, and even if they had tried to forget, the car crash would have been a daily reminder. He didn't want to even begin to think about forgiveness. That was never going to happen after what had been done to Sheppard and he knew it.

He drove on, unable to remember a time when he had felt more nervous of anything.

The road wound a little, and he had some difficulty locating the turning. The road was now unmade and he went slower as the car labored to cover the terrain. He had read the reports, every effort had been made to glean whatever small amounts of information they could about McKay and Sheppard, their lives together, the condition of the Colonel after the car crash that left him in critical condition with almost no success. McKay was good, his boast about being the smartest man in two galaxies was no idle one, and Sheppard's medical records were not available.

The property was fenced, the signs said electrified, and O'Neill had no doubt of that, the gate was also electric, with a key pad and a security camera. McKay and Sheppard were already holding the world at bay.

O'Neill pressed the button, they were here, if McKay and Sheppard gave them the brush off, his little group had tried…

He nearly jumped out of his skin when a voice answered.

"I've been expecting you." The tones were hard and flat, but he recognized McKay's voice. "You had better come in."

There was a soft beep and the imposing gates swing inward. O'Neill sighed. At least they had got on the property.

The drive swung gently down hill, curving around to the right, and the O'Neill had to hold back a gasp when he saw the house. If rumour was true, McKay had bought the land before Sheppard's crash, and when John was in the hospital, Rodney had hired an architect and a bunch of consultants to build them a home. A home adapted to the needs of a man likely to spend the rest of his life in a wheelchair.

Rumour also had it that Rodney then turned his enormous brain, and every last effort he had to research John's injuries, and put his lover back together piece by piece.

If the house was anything to go by, O'Neill had to give credit to gossip, the design aspects were clearly true.

The building was long and low, with plenty of natural light. No steps, and a wide doorway.

"I would say look what the cat dragged in, but our cats have better taste." The four of them jumped.

O'Neill's first thought was _there's no way this is Rodney._ The physicist was leaner and harder than he remembered. The tight dark jeans molded themselves to Rodney's body, the vest beneath the open Hawaiian shirt was dark blue to match the jeans and clung to Rodney's surprisingly developed pectoral muscles and hard, flat abdomen. His light brown hair was longer, curling at the back, and O'Neill had never seen the scientist's eyes so cold.

"McKay." Samantha Carter stepped forward.

"That would be Dr Sheppard-McKay to you." Rodney snapped. Clearly his previous interest in Sam was a dead end too.

Daniel shot a told-you-so glare at O'Neill and stepped forward. "Rodney, we're not here to upset you… Or John." He added hastily. "The Atlantis Project needs you."

The flash of something that looked like hatred burned bright in McKay's eyes just then, but his words were a surprise. "Daniel, we have no quarrel with you, this is just… difficult." Rodney sighed and raked a hand through his hair.

He shot a furious look at O'Neill and Carter. "I promised John that if we ever had to deal with this, we would both deal with it, and I would never try to hide anything from him or protect him. So, you had better come in." He turned, uncaring if they were following or not.

The house was everything O'Neill secretly hoped it would be. Testament to the love between the two men. Rodney had gone out and built it so that John would be able to cope with the long road to recuperation and rehabilitation.

"John's out on his run now, so I would appreciate it if you would lose the jackets, seeing you two is going to be hard enough without the added misery of his memories." Rodney waved a hand at the medal ribbons adorning O'Neill and Carter's uniform jackets.

Footsteps… "Rodney, I…" Sheppard's voice. O'Neill spun round.

His first thought, John was unchanged. Then he saw the panic flash through John's eyes, the nervous pause and he limped across to stand next to Rodney, now lit from the side wearing only a thin vest, board shorts and running shoes, his scars exposed it was worse than even O'Neill had imagined.

And there was real fear in Sheppard's eyes, the man was practically vibrating with tension. For the first time O'Neill realized the truth of the situation. John Sheppard's physical injuries had healed, well from the looks of things, but the trauma associated with the court martial which was obviously linked with the car crash in John's mind, that was something else altogether.

Rodney laid a gentle hand on John's shoulder. "John. It's okay. They can't do anything to you now." John's eyes darted from O'Neill to Carter and back, Woolsey and Jackson remained still not wanting to upset John further.

Sheppard relaxed into his husband's touch. "Sorry," he muttered thickly, "It's… you know…" he made a vague gesture with his hand.

"I suggest we take this into the lounge." Rodney's hand had moved to John's waist, and the lanky pilot almost huddled in to his embrace.

O'Neill glanced at his companions, this was going to be even tougher than he supposed.


	2. Ice Cold in Oregon

There were a few moments of awkward silence as O'Neill and the others followed Rodney and John into what Rodney termed the lounge.

Calling it a lounge really did not do the huge space justice O'Neill decided as he stared around. It was open plan, generously proportioned space, big comfortable couches occupied the space nearest the windows with an open plan kitchen behind and a large dining table off to the left.

Rodney sat down on the end of a couch, and waved at the space on couches, the visitors took their seats. Only John lingered, the tension hadn't left his body and he fidgeted a little before walking over to the window to stare out at the beach below.

"Fi will be here in half an hour." Rodney said, watching his husband, "why don't you get ready for her, darling?"

John nodded, shot Rodney a grateful look, and headed through a door just off the kitchen. Rodney watched until the door shut and then turned.

"Let me guess, something has gone wrong with the Atlantis Project. Probably on a catastrophic level, and you need me and John to fix it. Presumably because my brains and John's gene are the best and most viable options you have. The people behind this disaster have remembered one tricky little thing though, how they so thoroughly screwed us the last time. So they thought _let's round up General O'Neill and Colonel Carter_ and somehow we would be so delighted and grateful that the might of the SGC has deigned to notice us again that we would happily pack up and head back to Atlantis again without a second thought. And would you please lose the jackets, I think my husband has been unsettled enough so far."

O'Neill gaped. "Er… I wouldn't have put it quite like that."

"How would you put it?" Rodney was leaning forward, elbows resting on his knees, hands clasped, his head down. He looked up slowly. "More to the point why would you think that it would work?"

"Rodney. Please." Sam said. "No one means to hurt you."

Rodney got to his feet, "no? really? Well that's odd, because you tried to finish us both the last time."

"That was a mistake." Woolsey found his voice at last.

"A mistake?" Rodney's voice was deceptively soft. The blue eyes fixed Woolsey with a strange look. "You weren't there, it wasn't a mistake or an accident whatever the paperwork may say. John was on his way to find out if he was spending the next twenty years in prison, and that truck…" his fists clenched. "You know what the really sad part was, John was still prepared to give everyone another chance, he was so sure he would be acquitted because he had done nothing wrong and that Atlantis needed us as much as we needed her. But attempting to kill him…" Rodney shook his head, looked straight at O'Neill, "all he ever wanted to do was keep people safe, protect the city. He risked his life over and over and over again. You tried to destroy him for it, and you tried to use me as the weapon. Then when that wasn't working, a convenient car crash." His voice trailed off a little, and he got up to move to the window.

"We've built a good life here, we're settled, happy… we've finally managed to find some peace and maybe even some closure and John's getting better." Rodney turned back, "He cannot go through that again. And I know I can't."

"Rodney?" They all jumped a little, and O'Neill turned to see a young woman standing uncertainly in the doorway behind them.

"Fi." Rodney moved away from the window, "John's in the bedroom." She nodded, and something seemed to pass between them, a question asked, and answered.

O'Neill raised an eyebrow.

"Fi is a masseuse and nutritionist. She's been helping us for two years now." Rodney stared back, "oh my god, had you even considered that John's injuries might have been life-changing? That just maybe he wouldn't be up to this little trip of yours, or would it be that you know what John is like… that he would give everything he had and damn the consequences to his long-term health?" O'Neill watched as the familiar death-glare crossed McKay's features, but the actual hatred was new. "So that was it… drag us back by any means necessary, to hell with the consequences."

"McKay, no." Sam Carter moved then. "Rodney, Atlantis needs you and John." She knelt in front of him, took his hands, "we can't force you, we're hoping that…"

"You're hoping that we will conveniently forget a court martial, an attempt to actually kill John…" Sam looked into the burning blue eyes then and saw defeat.

"I don't know what it was like. Please Rodney."

"What it was like?" The rasp in Rodney's voice held her pinned. "Oh I'll tell you, then maybe you'll understand why you really aren't welcome here."

He pulled away from her, got to his feet and walked over to the window. "I got the call from the police about fifteen minutes after it happened. Don' know quite how that should have been, but we were infamous then, so perhaps it was no surprise. The truck…" his voice cracked, "the truck had hit John's Mustang side on, the driver's side was crushed." Rodney shook his head a little, "isn't this just like one of those mission reports, you know… the ones where we say how everything went to hell in a handcart, but that doesn't really cover it, how people died and nothing's ever going to be the same again."

Nobody moved or spoke. Acknowledging the truth of that.

"I had to watch while they cut John out of the wreckage. He was bleeding, and dying, and so broken I didn't know how to put him back together again. And then they came, and they asked me for permission to amputate. His leg… you see… it was crushed and broken and trapped… and I couldn't… I couldn't do that to him. So I told them no. And somehow they got him free. And all the way to the hospital, I thought I was going to lose him." Sam wanted to walk away, anything but listen to the broken sounds of Rodney's agony. As sharp as the day it happened.

"Nearly four years ago I didn't know if John would survive." Rodney's voice was clearer, less agonized, "three years ago, we weren't certain if John would ever walk again, two years ago we moved here permanently and in those two years we have found a good life, and a second chance. We have good friends, people who care about us, and we have each other. Physically John is not the man he was when you took us out of the project, his left leg is held together with rods and pins, and some cutting edge technological advances which I can't talk about…" Rodney glanced at Woolsey, "which are nothing to do with the IOA and are already patented, so don't even bother looking them up."

Woolsey shook his head in automatic denial, as though the IOA would take this man's achievement away. Then he remembered what they had done, and realized that they already had. John and Rodney had been the biggest threats to the IOA's position. Both men had poured their hearts and souls into Atlantis, and together they had achieved extraordinary things. Driving them out of Atlantis became an IOA objective.

The gentle thud of a fridge door closing had them all looking up. John held a big bowl of fruit, and his masseuse/nutritionist was holding something that looked like a bag of grass cuttings.

Rodney held up a hand.

"No citrus…" Fi rolled her eyes, "which you have been telling me almost every day for the last two years…"

"And no kiwi in Rodney's" John grinning at his lover.

"Because why would I want to drink anything containing a fruit that looks like a dead hamster." For the first time since their arrival, the visitors were relieved to see a genuine smile on Rodney's face.

"It's getting late." Rodney declared. "Coffee?" O'Neill practically surged off the couch.

"Yes. Please"

Rodney clapped his hands together. "Well, while I am getting coffee together, and organizing dinner, you can go and get your bags from the car."

O'Neill was startled. "Rodney, I…"

The McKay patented exasperated eye roll. "Please, genius here, and long time working knowledge of the habits of the SGC, and IOA, as if I didn't know you have over-night bags in the car." He stepped closer to O'Neill, "and use the opportunity to lose the uniforms, John is relaxed now, and I don't want you to push him into a flashback."


	3. Rodney's Actions

Sam Carter had changed out of her uniform, and since twiddling her thumbs until called to the dinner table really didn't appeal, she decided to take a little walk. Rodney had been perfectly civil, if angry, and it wasn't as though she was under house arrest. Maybe she would be able to pick up some clues to their life together.

The corridor outside her room was cool and contemporary like the rest of the house, white walls, which picked up the warmth of the golden wood beams and floors. McKay had had an architect design the space, but it showed Rodney's attention to detail in every possible way. The corridor turned and opened out into the beautiful big living space, but there was a room off the end that had intrigued her as she passed it when they were shown to their rooms. The door had been open and she had been afforded barely a glimpse in passing.

The room was large, light and airy, with a skylight and sliding glass doors out onto the deck. Two huge desks facing each other, with tables and filing cabinets and boxes fighting for space around the walls Apart from one clear expanse of wall. Sam moved closer.

Photographs, and certificates, all framed. The certificate from their civil ceremony announcing Dr M R McKay and Dr J S Sheppard… _Doctor_ Sam froze a little, why hadn't they known that.

"He insisted."

Sam turned. John was standing behind her. She took a moment to really look at him. The strong, confident, brave pilot, he was still all those things, but his courage was coming from a different place these days, and that hurt. The knowledge that he was so damaged.

"He said that I was good enough to finish the PhD, and since I had started and had nothing better to do, I should finish… Rodney's hurting." John moved a little closer, "he sees you come in, and he's terrified that we are going to be sucked back into the craziness and the politics." He stared at the wall, at the certificates and pictures, "you can see it all there. What he did for me. What I owe him."

He was standing beside her now, and she could see the scars, faded now, in some cases corrected with surgery, his temple, cheekbone, the scars continued down, shoulder, arm, down to the damaged leg. He put his hand out and touched his fingers to the frame nearest him.

"Rodney's bragging wall." Said Sam, since the majority of the certificates seemed to have Rodney's name on it.

"Mine." Said John. There was a little catch to his voice, and he put his hand out again to touch the nearest certificate in its neat frame. "My bragging wall. Have you ever had someone love you so much that they will do literally anything to keep you alive, to bring you back and make you whole again." She couldn't mistake the catch in his voice or the tears in his eyes.

She shook her head.

"Rodney did this for me."

Sam peered at the certificate. It announced in fairly bald terms that Dr M. Rodney McKay was certified as a Physiotherapist. Then she started to see. Rodney's PhD certificates were up there, and yes they were impressive, but every other framed certification took her breath away.

"Four years ago, they told him I would be a vegetable if I woke up. He didn't believe them. Then they said I would never walk again. He didn't believe them." Soft, breathy almost-laugh, "He didn't just not believe them, he set out to prove them utterly wrong. You know Rodney, he's so stubborn. He didn't just find the best in their field, he learnt all this stuff for himself so that he could help me. And when they couldn't fix me, he found another way to fix me."

It was hypnotic, hearing the depth of love expressed in John's voice and Rodney's actions. She put her hand on his arm, the left one, felt the warmth of his skin, and something else beneath the skin, her eye shot to the certificate on the wall again, to Dr M. Rodney McKay's third PhD… in robotics.

Sam stared down at John's arm, the warm skin beneath her fingertips, then up to his face, he smiled as the comprehension dawned in her eyes. "I'm still me, but some of Rodney's inventions have helped me in other ways."

"May I?" Sam wanted to feel for herself. "Reconstructive surgery?" John nodded, so she took his hand, and slowly and gently ran her hands up his arm feeling the unnatural structure beneath the skin, the places where the bone was reinforced, "wrist, elbow, shoulder… I didn't think that such reconstruction was possible."

"Without Rodney it wouldn't have been." John voice had a thread of steel, and there was a hardness in the hazel eyes that Sam was certain she had never seen before. She didn't know John could look so cold.

"Without Rodney McKay, I would have lost my left arm and leg. Without Rodney's stubbornness, and brains, and sheer force of will I would have been a forgotten footnote somewhere, kept alive until the insurance ran out and they made the decision to turn off the feeding tubes." He turned towards her, making his point "I will not let you just waltz in here and drag us down again. The IOA and SGC can swivel for all I care. The only way I am going back to Atlantis is if Rodney wants to. And that's a decision only Rodney can make."

Sam felt she should say something, but what to say.

"We're not here…"

"To coerce… I know, I heard the speech." John's smirk was a little cold, but not the hard, dead look that she had just experienced, "but be clear on this anyway Colonel, I will not help you push Rodney into agreement. But if he goes, I go with him as his husband. My military days are over, forever."


End file.
